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Final Report for WT, YH, and IS#8

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wtorous wants to merge 140 commits intoYu-Group:masterYu-Group/clinical-rule-vetting:masterfrom wtorous:masterwtorous/csi-pecarn-rule-vetting:masterCopy head branch name to clipboard

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Commits

Commits on Nov 19, 2021

• Added data

  

  William Torous

  authored and

  William Torous

  committed
  8157cc8

• Update readme.md

  wtorous

  authored
  66a08f3

• Copied template files

  

  William Torous

  authored and

  William Torous

  committed
  2317728

• Merge branch 'master' of https://github.com/wtorous/rule-vetting

  

  William Torous

  authored and

  William Torous

  committed
  9fb0755

• Update readme.md

  wtorous

  authored
  b1a056a

• Update readme.md

  wtorous

  authored
  ae68c90

• Some working EDA plots with poor code

  

  William Torous

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  William Torous

  committed
  c6e0b0f

Commits on Nov 26, 2021

• Initial report files and Will EDA

  

  William Torous

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  William Torous

  committed
  aef0f31

• Proper writeup file structure

  

  William Torous

  authored and

  William Torous

  committed
  ea26708

• Remove old report file structure

  

  William Torous

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  William Torous

  committed
  a6f86d0

• Added figs folder and test image

  

  William Torous

  authored and

  William Torous

  committed
  6119168

• Update readme.md

  wtorous

  authored
  85d7af4

• Draft introduction

  

  William Torous

  authored and

  William Torous

  committed
  e66002f

• Merge branch 'master' of https://github.com/wtorous/rule-vetting

  

  William Torous

  authored and

  William Torous

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  38af7a8

Commits on Nov 27, 2021

• Implemented dataset.py and added char to binary preprocessing

  

  William Torous

  authored and

  William Torous

  committed
  adff9f1

• Updated dataset.py file and proper loading in notebooks

  

  William Torous

  authored and

  William Torous

  committed
  bd72f8b

• Update readme.md

  wtorous

  authored
  51c7100

Commits on Nov 28, 2021

• Added robust covariates judgement call

  

  William Torous

  authored and

  William Torous

  committed
  d78a551

• Judgement call for Kappa data

  

  William Torous

  authored and

  William Torous

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  92937de

• Removed post-hoc variables and fixed indexing

  

  William Torous

  authored and

  William Torous

  committed
  3309827

• Update readme.md

  wtorous

  authored
  723a3e4

• Cleaned up Will EDA

  

  William Torous

  authored and

  William Torous

  committed
  f47339b

• Edits to dataset.py that didn't push for some reason

  

  William Torous

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  William Torous

  committed
  d803e08

• Fix bug in data indexing

  

  William Torous

  authored and

  William Torous

  committed
  88a62e4

• add impute_missing func

  imyaxuan

  committed
  b65f2c1

• Fixed some bugs in missing data imputation

  

  William Torous

  authored and

  William Torous

  committed
  1938bb1

• Code to remove single-valued columns

  

  William Torous

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  William Torous

  committed
  261ae54

• part of my eda

  imyaxuan

  committed
  89ee413

• Fixed bug in missing imputation and refactored code in a minor fashion

  

  William Torous

  authored and

  William Torous

  committed
  9df1d79

• Merge branch 'master' of https://github.com/wtorous/rule-vetting

  

  William Torous

  authored and

  William Torous

  committed
  da16df9

• Refactor code to work with multi-index

  

  William Torous

  authored and

  William Torous

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  241b254

• Update readme.md to Python 3.8

  wtorous

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  cb25359

• Example of how to use multi-indexing

  

  William Torous

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  William Torous

  committed
  a7de3e5

• Small update to MI example

  

  William Torous

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  William Torous

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  218acf9

Commits on Nov 29, 2021

• Update readme.md

  wtorous

  authored
  d24a7f3

• Added function to convert continous var to one-hot encoded

  

  William Torous

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  William Torous

  committed
  b5831f3

• Convert AVPU to one-hot

  

  William Torous

  authored and

  William Torous

  committed
  793cc48

• update eda

  imyaxuan

  committed
  a6856f9

• Merge branch 'master' of https://github.com/wtorous/csi-pecarn-rule-vetting

  imyaxuan

  committed
  a375365

• Data loading order change

  

  William Torous

  authored and

  William Torous

  committed
  f4c148f

• Partial function for splitting analysis var

  

  William Torous

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  William Torous

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  fb1f8fe

• Partial function for splitting analysis var updated comments

  

  William Torous

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  William Torous

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  00e7243

Commits on Nov 30, 2021

• Analysis variable pipeline complete

  

  William Torous

  authored and

  William Torous

  committed
  3b02a1e

• Proper column names when loading AV

  

  William Torous

  authored and

  William Torous

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  96096c8

Commits on Dec 1, 2021

• Added funcitonality to specify control type in get_data()

  

  William Torous

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  William Torous

  committed
  88503e3

Commits on Dec 2, 2021

• robust av parameter added

  

  William Torous

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  William Torous

  committed
  c85432b

• variable selection by tree(part)

  imyaxuan

  committed
  814c3df

• variable selection by tree update

  imyaxuan

  committed
  9979cef

Commits on Dec 3, 2021

• missing data plots

  imyaxuan

  committed
  1f53fb6

• variable selection by tree - update

  imyaxuan

  committed
  2b330ab

Commits on Dec 4, 2021

• variable selection - update

  imyaxuan

  committed
  42ae5c5

• some exploration on other tree methods - unfinished

  imyaxuan

  committed
  65ebee2

Commits on Dec 6, 2021

• try some specific but simple tree structure

  imyaxuan

  committed
  c1cccf9

• compare tree classifiers

  imyaxuan

  committed
  32a804f

• functions for tree methods

  imyaxuan

  committed
  660fcbf

• tree based classifiers

  imyaxuan

  committed
  353fcf1

• functions needed for simple tree algorithm

  imyaxuan

  committed
  36f64d8

Commits on Dec 7, 2021

• Covariates from full dataset

  

  William Torous

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  William Torous

  committed
  aecf20b

• Small encoding bug fixed

  

  William Torous

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  William Torous

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  86bead1

• Justification for GCS imputation; loads data with NA!

  

  William Torous

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  William Torous

  committed
  39ad7f0

• GGS 15 Imputations and added indicator

  

  William Torous

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  William Torous

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  05bf892

• Refactored GCS 15

  

  William Torous

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  William Torous

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  9fd8a83

Commits on Dec 8, 2021

• Robustness check for binary imputation

  

  William Torous

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  William Torous

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  2b003e7

• Indicator GCS NA and removed mean imputation

  

  William Torous

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  William Torous

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  bd2e347

• Fixed age bug

  

  William Torous

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  William Torous

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  26b5377

• Additonal GCS covar and JCs

  

  William Torous

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  William Torous

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  b7efedd

• VeryYoung with JC

  

  William Torous

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  William Torous

  committed
  5ecf7f8

• Improved GCS imputation

  

  William Torous

  authored and

  William Torous

  committed
  625e0bd

Commits on Dec 9, 2021

• Refactored data loading process for generating EDA plots

  

  William Torous

  authored and

  William Torous

  committed
  861402a

• Refactored Dataset() for clarity

  

  William Torous

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  William Torous

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  75d2950

• GCS thresholding JC

  

  William Torous

  authored and

  William Torous

  committed
  9e990de

• Update readme.md

  wtorous

  authored
  39ecd75

• Create data_dictionary.md

  wtorous

  authored
  a2e7110

• Update data_dictionary.md

  wtorous

  authored
  5da21bb

• Update data_dictionary.md

  wtorous

  authored
  a0d6e73

• Update data_dictionary.md

  wtorous

  authored
  61eb3dc

• Update data_dictionary.md

  wtorous

  authored
  c5cd9e3

• GCS imputation bug fixed

  

  William Torous

  authored and

  William Torous

  committed
  722a25d

• Update data_dictionary.md

  wtorous

  authored
  0be9f15

• Update data_dictionary.md

  wtorous

  authored
  581f33c

• Merge branch 'master' of https://github.com/wtorous/csi-pecarn-rule-vetting

  

  William Torous

  authored and

  William Torous

  committed
  6f70770

• Update data_dictionary.md

  wtorous

  authored
  bd469b4

• Code to generate data_description.md

  

  William Torous

  authored and

  William Torous

  committed
  c3471aa

• Manually remove some columns

  

  William Torous

  authored and

  William Torous

  committed
  feb4cd3

• Update readme.md

  wtorous

  authored
  01977e6

• Update readme.md

  wtorous

  authored
  b2a9d8f

• Update readme.md

  wtorous

  authored
  6ec99dd

• classifier comparison with age stratefication on complete variable list

  imyaxuan

  committed
  d91730a

Commits on Dec 10, 2021

• Judgements call for aggregation

  

  William Torous

  authored and

  William Torous

  committed
  83b6a4f

• Squashing bugs

  

  William Torous

  authored and

  William Torous

  committed
  3252bdb

• Less aggregation and flipped improved

  

  William Torous

  authored and

  William Torous

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  825e13c

• Covariate name change

  

  William Torous

  authored and

  William Torous

  committed
  5085ea8

• Fixed kappa JC

  

  William Torous

  authored and

  William Torous

  committed
  d1224b4

Commits on Dec 11, 2021

• Refactor for EDA clarity

  

  William Torous

  authored and

  William Torous

  committed
  1c8cdd9

• Code to generate demographic charts

  

  William Torous

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  William Torous

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  6543bea

• final model

  imyaxuan

  committed
  e395ed2

• final model

  imyaxuan

  committed
  aa7dc45

• Merge branch 'master' of https://github.com/wtorous/csi-pecarn-rule-vetting

  imyaxuan

  committed
  3c70234

• model functions

  imyaxuan

  committed
  63449dc

• notebooks for final classifier

  imyaxuan

  committed
  dcc82e7

• Older verison of code

  

  William Torous

  authored and

  William Torous

  committed
  cc20fe8

• Working JC dictionary

  

  William Torous

  authored and

  William Torous

  committed
  8f9d83c

• Working JC dictionary small change

  

  William Torous

  authored and

  William Torous

  committed
  2599871

• Update readme.md

  wtorous

  authored
  6ce64a1

• final model update

  imyaxuan

  committed
  f42e9f3

• Merge branch 'master' of https://github.com/wtorous/csi-pecarn-rule-vetting

  imyaxuan

  committed
  16b81cf

• Final functions with working JC

  

  William Torous

  authored and

  William Torous

  committed
  c9da782

• Merge branch 'master' of https://github.com/wtorous/csi-pecarn-rule-vetting

  

  William Torous

  authored and

  William Torous

  committed
  93c7b89

• Less JCs

  

  William Torous

  authored and

  William Torous

  committed
  b903669

• final model final update

  imyaxuan

  committed
  b446019

• final model final update

  imyaxuan

  committed
  5630631

Commits on Dec 12, 2021

• Update data_dictionary.md

  wtorous

  authored
  301ac33

• Update data_dictionary.md

  wtorous

  authored
  9710b64

• Added more comments to .py files and cleaned repo

  

  William Torous

  authored and

  William Torous

  committed
  2802868

• data_dictionry replaced in another location

  wtorous

  authored
  b688c4d

• Further cleaning up of code for submission

  

  William Torous

  authored and

  William Torous

  committed
  6e18834

Commits on Dec 13, 2021

• Figures for perturbation stability check

  

  William Torous

  authored and

  William Torous

  committed
  b598df0

• Updated function definitons to pass automated tests

  

  William Torous

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  William Torous

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  eaae9c0

• code for plot

  imyaxuan

  committed
  885f946

• update final model

  imyaxuan

  committed
  47186cb

• Update models to return 1D np array instead of list

  

  William Torous

  authored and

  William Torous

  committed
  8fa3e8b

• add print model

  imyaxuan

  committed
  a47a24f

• add print model

  imyaxuan

  committed
  381225f

• Updated model classes to pass tests

  

  William Torous

  authored and

  William Torous

  committed
  8db8572

• Will commit before outcome refactor

  

  William Torous

  authored and

  William Torous

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  5504132

• plot code

  imyaxuan

  committed
  03ca2a6

• Add eda

  ishaans99

  committed
  81b3998

• Add variable selection

  ishaans99

  committed
  c67a0f0

• Updated csi_injury to outcome to pass automated tests

  

  William Torous

  authored and

  William Torous

  committed
  37853b1

• Merge branch 'master' of https://github.com/wtorous/csi-pecarn-rule-vetting

  

  William Torous

  authored and

  William Torous

  committed
  b4fd9be

• Add writeup folder

  ishaans99

  committed
  17125a4

• Create requirements.txt

  ishaans99

  authored
  3602751

• Delete lab4 copy.Rmd

  ishaans99

  authored
  28c4c26

• Added Ishaan

  

  William Torous

  authored and

  William Torous

  committed
  37a239e

• Update data_dictionary.md

  wtorous

  authored
  025e2ae

• Update readme.md

  wtorous

  authored
  20b2669

• Added all figures

  

  William Torous

  authored and

  William Torous

  committed
  a1947af

• Add post hoc

  ishaans99

  committed
  4b58255

• Writeup and LaTeX source

  wtorous

  authored
  98b6ad1

• Update readme.md

  wtorous

  authored
  eafa809